Correlation of aberrant DNA methylation with cancer. Aberrant DNA methylation within CpG ‘islands’ is characterized by hyper- or hypomethylation of CpG dinucleotide sequences leading to abrogation or over expression of a broad spectrum of genes, and is among the earliest and most common alterations found in, and correlated with human malignancies. Additionally, abnormal methylation has been shown to occur in CpG-rich regulatory elements in both intronic and coding parts of genes for certain tumors. In colon cancer, aberrant DNA methylation constitutes one of the most prominent alterations and inactivates many tumor suppressor genes including, inter alia, p14ARF, p16INK4a, THBS1, MIT2, and MINT31 and DNA mismatch repair genes such as hMLH1.
Aside from the specific hypermethylation of tumor suppressor genes, an overall hypomethylation of DNA can be observed in tumor cells. This decrease in global methylation can be detected early, far before the development of frank tumor formation. A correlation between hypomethylation and increased gene expression has been determined for many oncogenes.
Prostate cancer. Prostate cancer is the most common malignancy among men in the United States (˜200,000 new cases per year), and the sixth leading cause of male cancer-related deaths worldwide (˜204,000 per year). Prostate cancer is primarily a disease of the elderly, with approximately 16% of men between the ages of 60 and 79 having the disease. According to some estimates at autopsy, 80% of all men over 80 years of age have some form of prostate disease (eg cancer, BPH, prostatitis, etc). Benign prostate hypertrophy is present in about 50% of men aged 50 or above, and in 95% of men aged 75 or above. It is obvious from these reports that prostate cancer is often not a disease that men die from, but with. Recent evidence suggests that the incidence of prostate cancer may in fact be declining, likely as result of better treatment, better surgery, and earlier detection.
Diagnosis of prostate cancer; molecular approaches. Current guidelines for prostate cancer screening have been suggested by the American Cancer Society and are as follows: At 50 years of age, health care professionals should offer a blood test for prostate specific antigen (PSA) and perform a digital rectal exam (DRE). It is recommended that high risk populations, such as African Americans and those with a family history of prostate disease, should begin screening at 45 years of age. Men without abnormal prostate pathology generally have a PSA level in blood below 4 ng/ml. PSA levels between 4 ng/ml and 10 ng/ml (called the ‘grey zone’) have a 25% chance of having prostate cancer. The result is that 75% of the time, men with an abnormal DRE and a PSA in this grey zone have a negative, or a seemingly unnecessary biopsy. Above the grey zone, the likelihood of having prostate cancer is significant (>67%) and increases even further as PSA levels go up. Numerous methods exist for measuring PSA (percent-free PSA, PSA velocity, PSA density, etc.), and each has an associated accuracy for detecting the presence of cancer. Yet, even with the minor improvements in detection, and the reported drops in mortality associated with screening, the frequency of false positives remains high. Reduced specificity results in part from increased blood PSA associated with BPH, and prostatis. It has also been estimated that up to 45% of prostate biopsies under currrent guidelines are falsely negative, resulting in decreased sensitivity even with biopsy.
TRUS guided biopsy is considered the ‘gold standard’ for diagnosing prostate cancer. Recommendations for biopsy are based upon abnormal PSA levels and/or an abnormal DRE. For PSA, there is a grey zone where a high percentage of biopsies are perhaps not necessary. Yet the ability to detect cancer in this grey zone (PSA levels of 4.0 to 10 ng/ml) is difficult without biopsy. Due to this lack of specificity, 75% of men undergoing a biopsy do not have cancer. Yet without biopsy, those with cancer would be missed, resulting in increased morbidity and mortality. Unfortunately, the risks associated with an unecessary biopsy are also high.
Molecular markers would offer the advantage that they can be used to efficiently analyze even very small tissue samples, and samples whose tissue architecture has not been maintained. Within the last decade, numerous genes have been studied with respect to differential expression among benign hyperplasia of the prostate and different grades of prostate cancer. However, no single marker has as yet been shown to be sufficient for the detection of prostate tumors in a clinical setting.
Alternatively, high-dimensional mRNA-based approaches may, in particular instances, provide a means to distinguish between different tumor types and benign and malignant lesions. However, application of such approaches as a routine diagnostic tool in a clinical environment is impeded and substantially limited by the extreme instability of MRNA, the rapidly occurring expression changes following certain triggers (e.g., sample collection), and, most importantly, by the large amount of mRNA needed for analysis which often cannot be obtained from a routine biopsy (see, e.g., Lipshutz, R. J. et al., Nature Genetics 21:20-24, 1999; Bowtell, D. D. L. Nature Genetics Suppl. 21:25-32, 1999).
Aberrant genetic methylation in prostate cancer has been observed in several genes including Gstp1, AR, p16 (CDKN2a/INK4a), CD44, CDH1. Genome-wide hypomethylation for example of the LINE-1 repetitive element has also been associated with tumor progression (Santourlidis, S., et al., Prostate 39:166-74, 1999).
Prostate cancer methylation markers. The core promoter region of the Gluthione S-Transferase P gene (GSTP1; accession no. NM—000852) has been shown to be hypermethylated in prostate tumor tissue. The glutathione S-transferase pi enzyme is involved in the detoxification of electrophilic carcinogens, and impaired or decreased levels of enzymatic activity (GSTP1 impairment) have been associated with the development of neoplasms, particularly in the prostate. Mechanisms of GSTP1 impairment include mutation (the GSTP*B allele has been associated with a higher risk of cancer) and methylation. However, with respect to the use of Gstp1 markers, the prior art is limited with respect to the number of Gstp1 promoter CpG sequences that have been characterized for differential methylation status. Moreover, there are no disclosures, suggestions or teachings in the prior art of how such markers could be used to distinguish among benign hyperplasia of the prostate and different grades of prostate cancer.
Aberrant genetic methylation has also been observed in several other genes including AR, p16 (CDKN2a/INK4a), CD44, CDH1. Genome-wide hypomethylation, for example, of the LINE-1 repetitive element has also been associated with tumor progression (Santourlidis, S., et al., Prostate 39:166-74, 1999).
However, use of these genes as alternative or supplemental diagnostically or otherwise clinically useful markers in a commercial setting has not been enabled. The application of differentially methylated genes to clinically utilizable platforms requires much further investigation into the sensitivity and specificity of the genes. For example, in the case of the gene CD44, a known metastasis suppressor, downregulation was associated with hypermethylation. However the use of this gene as a commercially avalable marker was not enabled, because it was also methylated in normal tissues (see Vis, et al., Mol Urol. 5:199-203, 2001).
Development of medical tests. Two key evaluative measures of any medical screening or diagnostic test are its sensitivity and specificity, which measure how well the test performs to accurately detect all affected individuals without exception, and without falsely including individuals who do not have the target disease (predictive value). Historically, many diagnostic tests have been criticized due to poor sensitivity and specificity. A true positive (TP) result is where the test is positive and the condition is present. A false positive (FP) result is where the test is positive but the condition is not present. A true negative (TN) result is where the test is negative and the condition is not present. A false negative (FN) result is where the test is negative but the condition is not present.In this context: Sensitivity=TP/(TP+FN); Specificity=TN/(FP+TN); and Predictive value=TP/(TP+FP).
Sensitivity is a measure of a test's ability to correctly detect the target disease in an individual being tested. A test having poor sensitivity produces a high rate of false negatives, i.e., individuals who have the disease but are falsely identified as being free of that particular disease. The potential danger of a false negative is that the diseased individual will remain undiagnosed and untreated for some period of time, during which the disease may progress to a later stage wherein treatments, if any, may be less effective. An example of a test that has low sensitivity is a protein-based blood test for HIV. This type of test exhibits poor sensitivity because it fails to detect the presence of the virus until the disease is well established and the virus has invaded the bloodstream in substantial numbers. In contrast, an example of a test that has high sensitivity is viral-load detection using the polymerase chain reaction (PCR). High sensitivity is achieved because this type of test can detect very small quantities of the virus. High sensitivity is particularly important when the consequences of missing a diagnosis are high.
Specificity, on the other hand, is a measure of a test's ability to identify accurately patients who are free of the disease state. A test having poor specificity produces a high rate of false positives, i.e., individuals who are falsely identified as having the disease. A drawback of false positives is that they force patients to undergo unnecessary medical procedures treatments with their attendant risks, emotional and financial stresses, and which could have adverse effects on the patient's health. A feature of diseases which makes it difficult to develop diagnostic tests with high specificity is that disease mechanisms, particularly in cancer, often involve a plurality of genes and proteins. Additionally, certain proteins may be elevated for reasons unrelated to a disease state. An example of a test that has high specificity is a gene-based test that can detect a p53 mutation. Specificity is important when the cost or risk associated with further diagnostic procedures or further medical intervention are very high.
The PSA blood test has a sensitivity of 73%, specificity of 60% and predictive value of 31.5%. PSA sensitivity and specificity can be improved but involve tradeoffs. PSA sensitivity can be improved by adjusting the “normal” PSA level to a lower value for younger men or by following serum PSA values in an individual patient over time (PSA velocity). Both methods will increase the number of cancers detected, but they also increase the number of men undergoing biopsy. Conversely, specificity can be improved by using higher “normal” PSA levels for older men, by using the free-to-total PSA ratio, or by adjusting the normal value according to the size of the prostate. These three methods decrease the number of unnecessary biopsies, but they increase the risk that some cancers will be missed.
It can therefore be seen that there exists a need for a means of prostate cancer diagnosis with improved sensitivity, specificity and/or predictive value.
Sensitivity and specificity of quantitative methylation-specific polymerase chain reaction (QMSP) assay alone (without histological analysis) in prostate cancer analysis of needle biopsies has ranged from 30% sensitivity and 100% specificity to 89% sensitivity and 64% specificity (Harden et. al. J Natl Cancer Inst 2003; 95: 1634-1637). However the predictive value of said technique as a clinical screening tool was not analysed. Furthermore, genetic testing of serum and bodily fluids such as urine and saliva would reduce the need for biopsies to detect cancer and would thus be the most effective screening or monitering tool. However the development of such tests requires an extremely high degree of sensitivity and specificity. Analysis of Gstp1 gene hypermethylation (Cairns P, et al. Clin Cancer Res 7:2727-30 2001.) in urine sediment of prostate cancer patients showed that only 6 out of 22 individuals with elevated methylation levels in biopsied tumors showed corresponding hypermethylation in urine samples.
Multifactorial approach. Cancer diagnostics has traditionally relied upon the detection of single molecular markers (e.g. gene mutations, elevated PSA levels). Unfortunately, cancer is a disease state in which single markers have typically failed to detect or differentiate many forms of the disease. Thus, assays that recognize only a single marker have been shown to be of limited predictive value. A fundamental aspect of this invention is that methylation based cancer diagnostics and the screening, diagnosis, and therapeutic monitoring of such diseases will provide significant improvements over the state-of-the-art that uses single marker analyses by the use of a selection of multiple markers. The multiplexed analytical approach is particularly well suited for cancer diagnostics since cancer is not a simple disease, this multi-factorial “panel” approach is consistent with the heterogeneous nature of cancer, both cytologically and clinically.
Pronounced need in the art. Therefore, in view of the incidence of prostate hyperplasia (50% of men aged 50 or above, and 95% of men aged 75 or above) and prostate cancer (180 per 100,000), there is a substantial need in the art for the development of molecular markers that could be used to provide sensitive, accurate and non-invasive methods (as opposed to, e.g., biopsy and transrectal ultrasound) for the screening of populations to provide an early diagnosis of prostate cell proliferative disorders.